rs9504552

Variant names:

• chr6-5846488-A-G
• rs9504552

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.263 in 152,094 control chromosomes in the GnomAD database, including 6,088 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40006 AN: 151976 Hom.: 6093 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.295

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.263 AC: 40013 AN: 152094 Hom.: 6088 Cov.: 32 AF XY: 0.268 AC XY: 19949 AN XY: 74332

African (AFR) AF: 0.121 AC: 5004 AN: 41512

American (AMR) AF: 0.388 AC: 5930 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3470

East Asian (EAS) AF: 0.165 AC: 851 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3565 AN: 10562

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20572 AN: 67972

Other (OTH) AF: 0.295 AC: 623 AN: 2112

Alfa AF: 0.282 Hom.: 2489

Bravo AF: 0.258

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9504552; hg19: chr6-5846721;